Connection
by Insanetrouble
Summary: One minute, Clara was standing behind the doctor listening to him ramble. The next, she was in a dark room with a feisty redhead, her parents and aunt, her husband and his father and a mysterious teenaged genius. Not to mention the one eyed woman and memory proof aliens. They don't know where they are, or why they've been taken but they do know there has to be a connection...
1. Chapter 1

"So... Where are we?" Grinned Clara, eyes flashing in excitement.

"Why don't you go look?" Challenged the Doctor, tugging on the red ribbon she'd tied her hair up with. Clara smirked, adjusting the ribbon before racing to the door and flinging them open. She opened her mouth, then shut it again, a look of confusion crossing her face.

"Er... Doctor? This isn't a planet... Why'd you bring me to an abandoned building in what looks like England?" She asked, the doctor frowned, bounding over and peeking outside.

"Oh. Oops." He offered sheepishly, causing Clara to roll her eyes, because really, she should have known he wouldn't end up in the right place. She straightened her dress and wandered outside, eyes roaming the desolate building eagerly. "Clara! Where are you going?!" The doctor asked crossly, scampering after her.

"You promised me an adventure!" She called over her shoulder as she peeking in through a window. The doctor sighed, scanning the building with his screwdriver and frowning slightly at the readings.

"Ooh, look at that! That's clever, isn't it?" He stared at the building in wonder, a bemused Clara watching him.

"Oi! Something you wanna share with the class?" She asked exasperatedly, and he turned to her with the screwdriver clasped in his hand and a wicked grin on his face.

"It's only abandoned on the outside! Inside, well, it's a hub of activity!"

"But... I just looked in, there's nothing there!"

"Well of course there's not! They couldn't just have anyone wander in and have a nosy round, could they?" He told her as he waved the sonic around a door, testing the lock as he did so. "Curious though. What would anyone do in 2030 with an abandoned building from the 2010's? Better to find a newer building, more equipped, less problems. Unless, of course, you didn't want to draw attention to yourself. Fly under the radar, as it were. Then, choose an old building in the middle of nowhere, keep the outside appearance the same and only change the inside, add only discrete security and limit the comings and goings and then bobs your uncle!"

He grinned broadly as he whirled around to face Clara triumphantly, only to find an empty space behind him.

"Clara?!" He called, stepping away from the newly opened door. His stomach twisted as his eyes lowered to the ground where the girl had just been standing. Hands shaking, he knelt slowly to pick up a red ribbon that lay on the ground, fluttering slightly in the breeze as he closed his fist around it. The same ribbon that had- until moments before- been tied in Clara's hair.

* * *

Clara groaned slightly as she opened her eyes, shifting as she registered the hard floor beneath her.

"It's ok. Take it slowly- you've been out for a while." With difficulty, she focused on a teenaged girl kneeling beside her, a worried look on her face. She had long, brunette hair that was pulled back tightly into a French plait, making it impossible to tell if it was curly, straight or somewhere in between with pale green eyes that seemed alight with... Something.

"Where am I?! How did I get here?!" Clara demanded as she shot upright, discovering use had no memory of ever coming here.

"Same way I did, I guess." The girl shrugged, settling back down against the wall as she crossed her legs. "Kidnapped."

Clara blinked at her indifferent tone. "And you're ok with that? Being kidnapped I mean?"

The girl raised her eyebrows. "It's hardly the first time, and I very much doubt it'll be the last. I'm AJ, by the way."

"Clara."

"Nice to meet you."

Before either could say anything else, the door opened with a loud clang, and a woman stepped through.

"Oh, good. You're awake." She said as her lip curled slightly.

"Kovarian." Groaned AJ as she hit her head against the wall with a curse. Clara looked at her nervously, sliding backwards from the woman with the eye patch as suited creatures began to enter.

"Jesus! Has anyone ever told you lot that you really need to see a plastic surgeon!?" Clara exclaimed, as she cringed away from the creatures.

"They're the silence." AJ muttered as she pressed closer to the wall, Clara mirroring her. The creatures advanced towards them, grasping them tightly as they hauled them to their feet.

"Hey! Let go!" Clara yelled as she struggled to free herself from their grip. Beside her, AJ was doing the same, wiggling desperately. The aliens took no notice, merely dragging them down corridors in a dizzying route that Clara knew she wouldn't remember even if she tried. Finally, they reached a single door at the end of a long corridor, which was quickly opened and they were thrown inside. Clara let out a yelp as she hit the floor, quickly twisting around to see the door close with a deafening bang, and the gap between it and the walls sealed so that kit simply looked like a smooth wall.

"Ah. That's a problem." Murmured AJ. Clara touched her head in confusion.

"Where... How did we get here?" She asked. AJ looked at her with wide eyes, open mouth giving no answer.

"The silence erase your memory the moment you stop looking at them. That's why you can't remember." A voice came from behind them and they whirled around to see a pale red head sitting against a wall next to a brown haired man. It was at this point Clara realised that there were several people in the room, all considerably older than she was. The only other thing apart from grey walls was a large mattress pushed against one, which the five were sitting together on.

"Who are you?" She asked. The red haired woman answered for all of them.

"I'm Amy. This is my husband Rory, my parents Augustus and Agatha, my aunt Sharon and Rory's father, Brian." Clara blinked at the onslaught of names.

"Er... Pleasure. I'm Clara and this is AJ." She introduced them both as she stood. AJ nodded at the group, running her fingers over the space where the door was.

"It's no good... We already tried. Only the silence or Kovarian can open it." Rory said, causing AJ to curse.

"It's a telepathic lock- only someone with a telepathic path to the door can open or close it. 63rd century technology to make it disappear just to double the challenge."

"Can you create a telepathic pathway?" Asked Clara. AJ nodded.

"Sure. If I had someone with a pre-existing path, a computer, several leads and wires and about a century." She answered, scowling slightly at the door. "There has to be another way out of here."

"There's not- we looked." Amy leant back against her husband, ignoring the helplessly confused looks from the other adults.

"Sure there is. You're breathing, aren't you?" AJ shot her an amused look, standing on tiptoe to run her fingers across the top of the walls.

"What?" Augustus asked.

"Of course!" Rory slapped his forehead. "There has to be a way for air to circulate, or we'd suffocate!" He jumped up and began to copy AJ, searching for the vent.

An hour later, they all flopped to the ground, finally admitting defeat.

"Alright. So no vent. How are they doing it then?" Muttered AJ, jumping to her feet and beginning to pace. Clara watched her from where she lay on the ground, mind running through the possibilities.

"Hey, slightly less important question- why are we all here?" She asked unhappily, unable to see a connection between herself, a teenager and the family.

"They took our son, but that doesn't explain why they kept us." Mused Rory. AJ's head snapped up.

"How old is he?" She asked.

"Six. Why?" Amy answered, straightening slightly as she studied the teenager.

"Because they took my seven year old sister too." AJ told them, biting her lip as she began pacing again. "Ok, kidnap his best friends, steal their son. Why? The silence. But he's already old enough to retain memories, so why not before when he could still be influenced? And why their family too?" She mumbled to herself as she paced, hands dancing through the air as she did.

"Wait! What did you mean, _his _best friends? Do you know the doctor?" Rory interrupted her. She came to a standstill and nodded at him.

"I'm assuming your family has too?" She questioned, mouth setting in a grim line when they nodded. She turned her attention to Clara, who nodded in agreement.

"I travel with him." She said softly. They all looked around at each other.

"That's the connection. The doctor." Amy spoke quietly, heart sinking as she looked at Rory. "He thinks we're stuck in New York in the 1950's. He won't even know we need help, and he has no reason to check up on our families."

"But he'll be looking for me" Clara said suddenly. They all looked at her, and she took a deep breath. "I travel with him _now. _I was standing right behind him when I was taken. He'll be looking for me! As long as we stay together, he finds me he'll find you!" She grinned triumphantly, and the others faces filled with hope.

"Er, slight problem? He can't see me." AJ interrupted them, causing looks of confusion.

"What?"

"I'm from his future. His very far future- he can't meet me yet, it would cause a paradox." AJ explained.

"No... As long as you're very careful about what you say it doesn't matter. We know a woman called River who used to do it. Don't answer questions and don't reveal you know about him and you'll be fine. By the time he realises he'll know not to say anything." Amy told her. AJ stared at her, before sighing loudly.

"My parents are going to kill me." She groaned.

_**Hello! This is my first Dr Who story, although I've been watching the show for a few years. Drop me a line to tell me what you think!? X**_


	2. Chapter 2

Clara opened her eyes slowly as she tried to remember where she was, the hard floor beneath her telling her she wasn't in bed. When she spotted the couple sleeping next to her and the teenage girl sitting cross legged in the middle of the room with her eyes closed, it all came back to her and she quickly sat up, wincing as her sore muscles protested.

"AJ? What are you doing?" She whispered, mindful of the sleeping group. The girls' eyes snapped open.

"Thinking." She whispered back.

"Oh." Clara nodded, rolling her eyes slightly. "Of course, silly me.

A ghost of a smile crossed the teenagers face, making her instantly younger.

"Can I ask you something?" Clara moved closer to her so she could whisper more quietly. The girl flashed a mischievous smile.

"You can ask." She raised a challenging eyebrow.

"What does AJ stand for?" AJ watched the curious woman warily.

"What makes you think it stands for something?"

Clara shifted uncomfortably. "Oh, I just assumed... I mean, it's not exactly a common name is it?"

"It stands for something. But... Spoilers." AJ shrugged sheepishly. Before they could say anything else, the door opened without warning, waking the rest of the sleeping group up.

"Good morning. I hope you all slept well." Kovarian entered with a sneer, gesturing behind her. Two of the silence came forward with a body wrapped in a blanket that completely covered it between them. Clara rose on her knees, reaching out to pull a frozen AJ closer to her and away from the creatures as they dumped the figure in the middle of the room. She rolled lifelessly and the blanket fell away, revealing a halo of blonde curls.

"River!" Cried Amy and Rory at the same time. The latter broke away from the group to rush to kneel at the woman's side, testing her pulse with practiced hands. Eyes still closed, she whimpered and flinched away from his touch, curling tighter into a ball. At this, Amy crawled over next to her husband to cradle the woman's head in her lap. She let out another whimper, eyes flying open to wheel around the room frantically. They came to rest on Amy's face and there was a flash of recognition.

"Melody?" Amy whispered, placing her hand on her cheek.

"Please. He's coming... The spaceman's coming! Help me, please!" The woman cried in a child's voice. Amy and Rory froze, eyes snapping to the smirking face of Kovarian.

"What did you do to her?!" Demanded Amy. Clara watched disbelievingly as the woman said nothing, face blank even when confronted with the unknown woman's obvious anguish and instead retreating from the room as Amy made to fly at her, stopped only by her husbands' hand on her wrist.

"She needs us." He said simply. Amy looked torn, glancing between the closing door and the woman on the floor. Coming to a decision, she nodded, sinking back down to sit next to her. The pair lent over her, Rory's hands ghosting over her in an effort to discover what was wrong with her.

Clara looked beside her to see AJ sitting stock still, eyes wide and shocked.

"Hey. You ok?" she murmured. The teenager turned to her, trembling and for a split second Clara didn't see an overconfident, feisty teen but a scared little girl. She was reminded for a second of Merry, from Akhaten. Both had the same, lost look in their eyes.

"I'm... I'm fine." AJ said, clenching her trembling fists in an effort to still them. Clara was about to pry further, but the woman suddenly screamed, writhing as she rolled away from Rory and Amy.

"Please! Please!" Rory started towards her, to where she'd hit the wall and stopped, sobbing as she cringed away from all of them but was halted by Amy, who held up a hand to stop him as she stood and walked slowly to where the woman lay against the wall. She lowered herself carefully, slowly, treating the woman as you would a wounded animal.

"Melody? Melody, it's ok. You're safe, I promise." Amy spoke soothingly, and the whole room seemed to hold its breath as she attempted to calm the hysterical woman.

"Help me please!" Melody sobbed.

"Melody!? Look at me. Look at me sweetheart." Amy's voice seemed to break through to her, and terrified eyes turned her way. "You are safe. I'm not going to let anyone hurt you, ok? I need you to trust me though, because we can't help you if you don't."

Amy stretched a hand out, slowly. Melody studied her face for a moment, tears still on her cheeks before ever so carefully, she stretched her own hand out and placed her fingers on Amy's, prompting a smile from the redhead.

"What's happening to me?" Whispered Melody. Amy smiled reassuringly.

"I don't know, but we're going to find out ok?" Melody shook, fingers tightening. Just as Amy began to move towards her, a loud bang from outside the room echoed and Melody let out another shriek, ripping her hand away to press herself against the wall. She fell, body shaking violently as she let out anguished screams.

"Protect her head!" Rory ordered as he began to test her reactions, so Amy cushioned her head carefully, leaving the rest of her body to shake and twist. This new screaming seemed to break AJ from her reverie and she bolted over, using her hand to block and release light to Melody's eyes.

"She's trapped inside her own memories." She mumbled.

"What does that mean!?" Cried Amy frantically over the screams.

"It means they did something to her that's regressed her memories back to when she was a child! She's not in reality anymore; she's reliving some of the worst times of her life over and over again, and all inside her own head! It's the perfect prison- no escape, no time to think clearly or even coherently, no way out." Snapped AJ as she began to pace, running her hands over her hair in agitation.

"Can we stop it?" Ever the calm one, Rory's voice was raised only to be heard over the noise.

"I don't know! Amy, try to calm her again! It worked last time." Amy began to murmur softly to the sobbing woman, who began to calm almost immediately until her screams became soft cries that eventually faded out as she slipped asleep. AJ turned, frowning as she caught sight of the shell shocked people sitting on the mattress. She shoed them off and Rory slipped his arms around Melody and lifted her onto it gently, stroking her face lightly.

"Melody- that's her name? And I'm assuming she knows the doctor too?" Asked Clara quietly.

"Her name is Melody, yes, but she only answers to River. And yeah, she does." Rory answered her, wiping his brow.

"River?" Clara questioned. Amy grinned faintly.

"Long story. Just go with it."

"Melody... Like Mels?" Asked Agatha suddenly. Clara frowned as she watched the couple exchange uneasy looks at the question.

"Mum-"Amy started, but was quickly interrupted.

"No Amelia! You've been missing for eight years! Then I get kidnapped, and find you and your husband perfectly fine and apparently unconcerned with the lack of contact. There's a lady who seems to enjoy tormenting you and several others who all seem to know your not-imaginary friend and holes in my memory and a mad woman with the same name as your missing best friend and we're locked in a door less room and I would like to know _what is going on_!" Agatha took a deep, gasping breath which seemed unnaturally loud in the silent room.

"Mother, I think you might want to explain to them what's going on." A quiet voice came from behind them. Clara glanced back at Melody- no, _River- _who was now awake, calmly lying watching them exhaustedly with amused eyes, head cushioned on her arm. Thankfully, with no sign of a memory relapse.

"Mother!?" Agatha spluttered. Amy sighed, going and settling next to River and begun to speak.

"Let me tell you a story. An amazing, impossible story of a brilliant mad man who stole a magic box, and a little girl he met in a garden one night. A story of love, and loss, of hate and fear and hope. Of traps and trials and joys and triumphs, of impossible things and incredible stories but most of all, of courage, and bravery." As she spoke, she stroked the hair of the woman whose head lay in her lap, her husband smiling knowingly at her. "A story that is absolutely true..."

**_Hi again! I probably should be revising for my law gcse, but hey, this is much more fun! Thanks to everyone who reviewed, and please tell me what you think of this one! X_**


	3. Chapter 3

Clara lent back against the wall as she considered the story she'd just heard. Amy had talked for hours, describing her journeys with the doctor and how Melody had been born, right up to their current life in Manhattan, with Rory and River adding in snippets here and there when needed but Clara had noticed there were disjointed bits, or parts that weren't explained properly, like how River and the doctor had reset the universe in an alternate timeline. It hadn't seemed to bother anyone else though; AJ had remained strangely silent throughout it all, and Clara noticed that none of the red-haired woman's revelations seemed to come as a particular surprise to the teenager. In fact, she considered, AJ had seemed almost bored with the story.  
Clara felt waves of nausea come over her and she fell to her knees. Which was strange, considering she'd already been sitting down a minute ago. She opened her eyes to find herself in a different, much larger room in a cage, the rest of their little group with her.  
"How did we...?" She twirled on the spot, confused.  
"The silence. Memory erasers, remember?" Rory clambered to his feet, swaying slightly. Bright lights shone through the room, making it difficult to see. Clara peered out to see consoles, but as she tried to step towards them, pressing herself against the bars in the process a sharp shock ran through her body.  
"Ow! There's some kind of current running through the bars..." She told the others, reaching out her hand carefully to test it.  
"They're doing it on purpose." Said AJ grimly. "They're disorientating us so we question everything. Moving us when we can't remember, using unsettling techniques, changing scenarios just as we begin to get used to them. Which is good!" She whirled around with a grin after glancing venomously at the bright lights.  
"Good? Ah... Sorry love, different wavelength here. How is it good?" Clara asked with a raised eyebrows.  
"Because it means they're nervous! They think we're good enough to beat them if we're left alone. They're especially scared of Dr Song, so scared they've tried to wipe her memories and trap her inside her own mind. Good news, them being scared means they're making mistakes and know we're better. Bad news, they seem to be succeeding with River and have also increased security, making it difficult for anyone to get in or out."  
Clara blinked slightly at the rapid fire answer, mind taking a minute to process what had been.  
"Tick tock goes the clock we laughed at fate and mourned her. Tick tock goes the clock till River kills the doctor." River mumbled. AJ frowned, leaning forward to hear what she was saying.  
"Damn. They must have had us out longer than we thought and done... Whatever it was they did last time to her again." She scowled slightly as she jumped up and once again began to pace.  
"You know, Amelia, despite your stories she doesn't seem like very much." Sharon peered down her nose at River Song.  
"Well, she is. She's amazing." Rory told her with steel in his voice. Sharon raised an eyebrow at him, but said nothing. AJ was ignoring them, fingers fiddling with the end of her plait as she continuously moved.  
"Ok, I believe that the only way to stop a terrible secret being revealed is to kill the man who holds it. So I kidnap a baby who just by chance happens to have time lord DNA, brainwash her, turn her into a psychopath and order her to kill. That fails, so I force her to do it against her will, which also fails because the doctor saves himself. I then wait years, before re-kidnapping said baby, and her parents and their parents along with his current companion and two girls from the future. To do so I risk tearing apart reality- again- or creating a paradox and then take a six and seven year old who are too old to be brainwashed and too young to be of any use. Why?" She rambled aloud.  
"Tick tock goes the clock he gave all he could give. Tick tock goes the clock now prison waits for river." River sang morosely.  
"Yes, thank you dear." AJ said distractedly. Clara frowned.  
"What if it wasn't about the children? What if they were taken to ensure we wouldn't escape, and we're all here for something else?" She suggested.  
"But why take Fae and I as well? We're from the future, the doctor doesn't even know we exist yet. Why bring us here?" AJ continued to pace.  
"A trap to kill the doctor?" Suggested Amy. "No, wait. Same problem..."  
"And why take us?" Sharon spoke up, and Augustus nodded in agreement.  
"We only met the man once!" He reasoned.  
Suddenly, the lights flickered and dimmed, allowing them to see that they weren't alone in the room, with the aliens of the silence scattered periodically throughout.  
"Well well. Seems like your precious doctor doesn't care as much as we thought." Kovarian came into view, lips twisting in a parody of a smile. "After all, where is he?"  
"You have no idea what you're doing." Amy told her coldly. "He'll come, and he'll win. Just like he did all the times before. It must be pretty embarrassing to find the man you'd declared officially dead is actually alive and well, huh?"  
"Oh, Amelia Pond. So brave, so believing. Tell me, Amy, how many times did he betray you? Let you down, leave you? Disappoint you?" Kovarian's voice got progressively quieter until she was almost whispering, leaning closer to Amy so she could hear. "He doesn't care. Look at your darling Melody. Tortured and screaming, crying out for him to save her but yet he doesn't come. Not even for his wife." She spat, pushing away from the cage suddenly as she sneered back at them.  
"He'll come." Amy said simply. Kovarian turned and walked out with the aliens following her, but left the lights dim. Amy turned, a smug smile on her face.  
"Amy...?" Rory rose to his feet, confused as to why his wife would be happy. The smile never leaving her face, she slowly let a long object slip from her sleeve. Clara looked closer, and saw a remote of some kind, which she assumed was good judging by the way AJ laughed when she saw it.  
"You picked her pocket!?" she grinned. Amy shrugged, but couldn't keep the smile from spreading across her face. Clara scrambled up from her seat on the floor as Amy studied the plastic object, before pressing a button. The lights brightened, and blinded them all. Behind her, Clara could hear Amy fumbling with the remote until they lowered again, and then, suddenly, a portion of the cage swung open.  
"Found it." The redhead announced unnecessarily. AJ bounced over to the nearest console and immediately began typing rapidly, frowning in concentration while Rory lifted River and bought her out form the cage.  
"Kovarian always did underestimate everyone else." Amy said, a note of proud satisfaction in her voice.  
"Got it. This place is huge- stretches for about a mile square, all underground and consisting mostly of tunnels connecting seperate rooms. There's a room that's using a lot of power- more than any other. One door to a single tunnel that has only one way in or out, that opens only twice a day, everyday. If I had to guess, i'd say that was where they're keeping the children."  
"Well, that's good right?" asked Amy. "We go, grab the kids, get out of here. Contact the doctor, tell him we're all right. We get back to the 1950's to avoid a paradox, Clara goes back on the tardis, Mum, Dad, Brian and Aunt Sharon go home and you go back to your time, then everyone's happy, yeah?"  
AJ winced slightly, hesitating. "The room's on the other side of the compound. Even if we could get there without being noticed- which is unlikely, may I add- we'd have to double back almost a mile with two kids to get to the exit. It's practically impossible." Amy shook her head angrily, backing away from the teenager in frustration.  
"Then what do we do!?" she yelled. "That's my son! I already lost my daughter, I can't lose him as well!"  
"Your daughter is right there!" AJ shouted back at her, standing from the chair she was sitting on. They all looked at her with shock, but she had eyes only for a stunned Amy, fire blazing within them. "She's right there. Maybe you didn't raise her, maybe you don't know her as well as you'd like but she's still your baby. And don't you forget that, because she needs you. Do you have any idea how much it hurts to look into your parent eyes and see that they don't have a clue who you are? To know you haven't been born yet from their point of view? Because take it from me, it feels like somebody's ripping your heart out of your chest just for kicks, so don't you dare think for one minute that this is easy on her, that it doesn't matter who she is. Because it does." They stared at eachother for a long moment, before AJ abruptly turned on her heel and walked to the other side of the room where she deftly entered a code and opened a cabinet.  
"Catch." She chucked various items back to their owners, slipping some into the pockets of her leather jacket and belt. She closed her fingers around two items at the back, withdrawing a handheld console and a vortex manipulator and a small, slow smile appeared.  
"I think I know how we can do it." She held them up with a slight grin. "Cheap time travel, but in the absence of anything else..."  
"We can get the children, and get out of here in the space of three seconds!" Rory grinned broadly, leaning over to hug Amy. AJ slipped the manipulator around her wrist.  
"It can only carry three at a time, so I'll bring them both back here first." She told them, beginning to key in the coordinates. Before she could, a familiar whirring sounded throughout the room and the Tardis materialised, while at the same time the doors flung open and Kovarian strode in, members of the silence flanking her.  
"This is bad. This is very very bad." Muttered AJ as she retreated to stand next to the others, fingers fiddling with the gun she pulled from her pocket as she did so. Rory crouched over an unconscious River protectively while Amy and the others stood in front of both of them, blocking them from the silence and Kovarian.  
"Do not take your eyes off of them." Amy warned. Following her instructions, Clara walked carefully backwards until she reached the tardis, where she banged on the door as loud as she could.  
"Hey, chin boy! Hurry it up would ya?!" she yelled as she moved a few steps away again, eyes fixed on a smirking Kovarian. The doors were thrown open with a flourish to reveal the doctor.  
"Clara! I swear, i'm going to get a leash for you if you make a habit of this!" he hugged her fiercly, lifting her into the air and she yelped slightly, laughing.  
"What?" she protested,  
"Disappearing! Vanishing, getting into trouble! Honestly, every time I take you out, and sometimes when I don't!" she let out another laugh at his indignant expression.  
"When you two have quite finished, maybe we could get back to the memory proof aliens?" Amy called testily over her shoulder, still not taking her eyes from the creatures. The doctor froze, turning slowly as his hands fisted tightly, swallowing thickly before he managed in a weak voice-  
"Amy...?"


	4. Chapter 4

"Amy…?"

"Hey raggedy man." She said softly, heart clenching even as she kept her eyes firmly on the creatures in front of her. He spluttered disbelievingly, for the first time looking around at the rest of the room.

"You. You did this." His eyes fixed on Kovarian, and her lips twisted.

"Hello doctor."

"What have you done?" he demanded. "You could destroy time!"

"Oh, it's always the same with you, isn't it?" Kovarian sighed. "This could all have been avoided if you'd just _died._"

"Did my best dear, I showed up. Wait, I'm repeating myself. That's not good. Always be original I say."

"Doctor!" Amy said through gritted teeth. AJ rolled her eyes slightly, keeping gun levelled at Kovarian.

"I have a shot if you'd like me to take it." She said evenly, voice as steady as her hand. The doctor spun to look at her in surprise.

"No shooting! They'll just kill you!"

"Well, I hate to tell ya but they're going to do that anyway!" the teenager snapped.

"Oh, we're not going to kill you. Not yet anyway. Although I make no promises about little Melody- I'm afraid she's caused too much trouble already." Kovarian said sweetly, gesturing to the woman the doctor was now noticing for the first time.

"Oh, shut up you old cow! Doctor, she did something to River. She… what was it AJ?" Amy interrupted them, a note of fear in her voice when she mentioned her daughter.

"Forcible memory regression with a mental loop concentrated in memories accompanied by a rise in adrenaline, epinephrine and nor epinephrine with cortisol as well as increased pulse and blood pressure." Kovarian's mouth tightened as AJ confidently reeled off what was basically a guess, confirming she was right. The doctor looked mildly impressed, but before he could say anything Kovarian spoke up.

"It's time. Bring them through." As she walked out the silence advanced on them, hissing, surrounding them. AJ fired shot after shot at them, each hitting its mark dead on, but for every creature she hit another appeared.

"Rory!" Amy screamed as two silence began to drag him away as he struggled to get back to River, and she lunged away from the cage of her own fathers arms to try to get to him. She hit out randomly, before being forced to the ground, still yelling and screaming. Her parents and aunt both followed suit, their voices filling the room like a bad horror film. Despite their fighting, however, the silence overpowered them, gripping their arms to drag them through to the next room.

"Oh my…" Clara breathed, stilling. A raised platform stood in the centre, surround by a semi-circular console. On the platform, a central circle was surrounded by several others, all evenly spaced as wires hung down randomly here and there. On one side, where there was a space in the console a table sat with straps on, the purpose of which nobody needed to guess at.

The silence dragged them forward, depositing each into one of the separate outer circles, which immediately shone with a light that none of them could cross. All apart from River, who was dragged to the table and strapped in, head rolling as her eyes flickered dozily.

"What are you doing?! What is this?" AJ yelled as she rolled to her knees, fear on her face. Kovarian reappeared, leading two scared children by the hands.

"Fae!"

"Anthony!"

Both the children looked up hopefully, and tried to run to the group but Kovarian yanked them back harshly.

"Momma! Daddy!"

"Li!"

Kovarian wrenched Fae to the centre circle when she tried to run to AJ, pushing her in as Anthony was shoved into the only remaining outer circle.

"Leave them alone!" Amy shouted desperately. Kovarian smirked, turning back to an unconscious River.

"Oh Melody. Wakey wakey." She sang, trailing her fingers over her face. When she stirred, but didn't open her eyes Kovarian frowned and pinched her face viciously. River's eyes flew open with a gasp, and she cried out when she saw Kovarian, desperately trying to free herself from the confines of the straps. "Oh, shush now Melody." Kovarian cooed.

"Get off of her!" Rory was furious.

"Kovarian! What are you doing?! You have me, leave them all alone." The doctor called desperately, but Kovarian just laughed humourlessly.

"But where's the fun in that, doctor?" she moved towards Fae, who shuffled back as far as her invisible cage would allow, glancing constantly at AJ for reassurance. Clara was struck at how similar the sisters looked, with the same coloured hair and eyes. Fae's hair, however, was shoulder length and had hints of red throughout while AJ's was much longer and had natural blonde highlights that shone under the harsh lights above.

"Madame Kovarian! Leave her alone, please!" River shouted as she struggled against the straps holding her down.

"Stop this! Stop it right now!" The doctor roared, testing the confines on the barrier, trying to find a weakness. It was futile however, and he soon gave up, staring in horror as machines began to whirl around them, focusing on Fae, who screamed and cowered away from them as arms and pincers advanced towards her.

"Kovarian!" The doctor was livid, fists clenched as he pounded against the barrier.

"What are you doing to her?!" AJ yelled frantically. Kovarian smirked.

"Honestly. Haven't you worked it out yet? Clever little AJ, with her big brain but nothing much else? Such a disappointment, so much so her parents abandoned her because she wasn't good enough."

"Shut up." AJ dug her nails into the palm of her hands, glaring in hatred at the one eyed woman, who let out a delighted laugh.

"Touched a nerve, have I? Oh well, I'll give you a clue. D. N. A." Kovarian enunciated carefully. At the lack of comprehension, she sighed heavily.

"Really? OK, another clue. Universe's." Confusion passed over AJ's face, but was quickly replaced by a look of horrified realisation as she stared at the machines.

"Oh no..." She whispered.

"What!? What are we missing?" An exasperated Clara asked. AJ looked at her, then back at Kovarian before her eyes fixed on Fae.

"She's going to try and return to the previous universe!" at their blank looks, she quickly explained as Kovarian watched on, smirking. "The story Amy told, about the cracks in the universe? Well, that universe was riddled with holes and problems which were all fixed when the doctor flew the Pandorica into the exploding tardis. Well, the crazy psychopath is going to try and reverse it so those problems reappear. Fae was conceived in the altered timeline, her DNA wold make it possible."

"It will never work! It only happened because the tardis exploded, and that won't happen again!" River exclaimed, the doctor slamming his hands against the invisible barrier, much to Kovarian's amusement.

"Too late, doctor." Kovarian said, as the machines descended, and one lowered to grip Fae, who had fallen silent but was white as a sheet, holding her still. As she was pinned down, her mouth fell open in an unheard scream.

"Stop! Stop it! Kovarian! Stop it, use me instead!" AJ screamed, tearing her eyes away from her sister to look at the conniving woman.

"Oh, little AJ. So eager to protect. Sorry dear. I need her DNA- yours is no good."

"You're wrong." AJ slipped her hand under her shirt and brought out a chain. Clara peered closer to see what looked like a key on the end of it, but before she could look properly AJ ripped it from her neck and stuffed it in her pocket, never breaking eye contact with Madam Kovarian. As soon as her fingers had come out of contact with the chain, the machines began to beep erratically, and Kovarian looked up from a screen, stunned.

"How is this possible?" she hissed, advancing on AJ, who smirked.

"What's wrong, madame Kovarian? Not quite as clever as you thought you were? Perception filter dear. Beat your silly little machines without any effort at all." She said smugly. The doctor smirked, and River let out a surprised chuckle at the girls audacity. Kovarian let out an angered screech, and quickly disabled the barriers surrounding the two sisters. Fae let out a sob, running into AJ's arms without hesitation. The elder of the two whispered comfortingly to her younger sister.

"It's OK. I promise you, it's going to be OK. Remember the stories, yeah? All the ones I told you- never forget them sweetie. Because you're going to need them." Kovarian dragged Fae away to where AJ had just been and activated the barrier, before turning back to the teenager.

"You know something Kovarian? My parents always told me there was one thing you never understood. And they were right. You don't understand it at all, do you? I always thought you did, on some level but I was wrong. That doesn't happen very often."AJ mused aloud, walking around the centre slowly. Kovarian moved with her, eyes narrowing.

"Oh? And what's that?"

AJ smirked.

"Love." She said, before withdrawing a hidden gun from inside her jacket and blasting the compute hub beside her. A shower of sparks lit the air, before a deafening bang filled the room, and the electronics exploded in a whirlwind of colours that quickly faded to black.

**_This was surprisingly fun to write... not sure what that says about me! Please review and tell me whether you're liking it or not! X_**


	5. Chapter 5

**_Who watched the finale last night!? How we're supposed to wait till November I do not know. On the plus side, the inspiration it's given me means you've all now got extra scenes in this story and a sequel that wasn't at all planned!_**

**_Tell me what you think of this one!? X_**

Clara groaned, trying to move as little as possible as she woke.

"Ow." She mumbled, shifting slightly. She cracked open her eyes to find the room in relative darkness, the only light coming from a single screen on the console on the other side of the large room, but even that was flickering and weak.

"Hello?" she called quietly, trying to see through the gloom. When no answer came, she felt a flicker of fear run through her. She shifted so she was sitting up, confused as to where exactly she was- she was pretty sure she's been thrown across the room in the explosion. She gasped as a hand came down over her own, but relaxed as she heard the doctors' voice in her ear.

"You have to stay quiet. We're not sure where the silence went, or Kovarian." His breath tickled her as he whispered only just loud enough to be heard. She nodded, knowing he would feel the movement and he helped her carefully to her feet, hands on her waist to steady her. It was then she noticed he'd covered her thin dress with his jacket and he now slipped it around her shoulders, nudging her arms as encouragement to slip them through the sleeves.

Suddenly, a beam of light pierced the darkness. Clara shielded her eyes from the beam, and the whispered apology told her it was Rory behind the torch. He shone it around the room, searching the corners and the ceiling for any signs of the memory-proof aliens, but on finding none he simply shone it along the walls to look for an exit.

"Right, have we got everyone?" the doctor called all of a sudden, making Clara jump violently. She pressed a hand to her chest where she could feel her heart racing.

"I think so- I have River's hand in mine and AJ's with Brian. Everyone else is conscious" Amy answered with a distinctly icy tone in her voice, although Clara couldn't see her expression.

"What about the children?" she asked, her natural instincts taking over.

"I'm with Mummy too." A boys' voice piped up.

"And I'm here!" Fae said.

"Where's here, honey?" Amy asked. There was silence for a moment.

"Um… by the screen?" Rory shone the light over and found the girl curled up, blinking blearily in the bright light. Clara made her way over to kneel and slip her hands through the girls'.

"Right then. Best thing we can do is back to the tardis, which is only next door. It's safer there and I can do med scans on everyone, check for damage." The doctor said decisively. "I'll carry River."

"That won't be necessary. I can carry her." Rory told him sharply, handing him the torch and slipping his arms around the unconscious woman. The doctor sagged slightly, but lifted AJ instead and led the way back to the tardis.

"Cool!" Anthony yelled as they entered. He broke free from Amy's grasp and raced forward, eyes alight with wonder as he spun on the spot. The doctor chuckled, walking through to the medical bay and placing AJ on the bed. Fae scampered in after him and Rory, still clutching Clara's hand. As the girl touched her sister's hand and tugged it slightly, the teenager began to wake.

"Ouch."

"Hang on two ticks AJ, while I scan River and then I'll be with you." The doctor bustled around the bed where Rory had laid the blonde, barely glancing over at her.

"Oh, you care now do you?" Amy said tartly as she entered with her son on her hip. She passed him to Rory as the doctor spun on the spot.

"What's that supposed to mean?" Hurt, he stroked River's hair absently as he faced Amy, who crossed her arms furiously.

"Oh, don't give me that! You couldn't even be bothered with her earlier until Kovarian pointed her out! Kovarian, of all people! I left her because I assumed you would keep her safe, doctor! Instead you didn't even realize she was missing! She almost _died _saving you, she gave up _centuries _of her life! I understand you have wonky timelines, but how could you not know that monster had taken my baby _again!_ " Amy was now close to tears, screaming at the doctor and pounding at his chest, but as he wrapped his arms around her and held her close she dissolved into sobs, clutching at him desperately.

"Oh, Amelia. My Amelia." He murmured into her hair, holding her just as tightly. After a while, Rory cleared his throat awkwardly.

"Husband!" he pointed out. The doctor released a now calm Amy, pressing a kiss to her hair.

"I would never, ever not keep her safe." He whispered, and Amy nodded tearfully.

"I know, I'm sorry. But I was just kidnapped from a timeline I shouldn't have been able to leave. It's a little disconcerting; I'm allowed to be emotional." The doctor chuckled, turning to Rory with open arms.

"Rory the Roman!" he hugged him fiercely, which caused Anthony to laugh at the expression on his fathers face. The doctor knelt beside the boy.

"Hello. I'm the Doctor." Anthony looked at him solemnly, but then slowly broke into a smile, laughed and hugged him, throwing his arms around his neck with the innocence only a child could have. "Oh!" the doctor flailed slightly, but eventually gently hugged him back.

"Normal children get bedtime stories of the three little pigs. Anthony got the mad doctor in a stolen blue box." Amy explained as she sat on the edge or River's bed.

"Doctor, River will be OK, won't she?" Rory asked.

"The tardis is scanning her now but it may…"

Clara sat on the end of AJ's bed with Fae in her arms, still wearing the doctors' jacket and watching the reunion wistfully. The love the group had for each other was obvious, despite their rather strange dynamics.

"AJ?" Fae's voice broke through her thoughts, and she turned her attention to the sisters.

"Hm?"

"How are we going to get home?" The young girl asked. AJ smiled gently.

"Same way we always do sweetie. Call mum for a lift." She winked, and Fae giggled, a shy smile crossing her face and just then, the tardis let out a series of beeps.

"Ah ha!" The doctor jumped up and checked the screen. "Ooh, nasty. Rory, Amy, your daughter will be just fine. Maybe with a few extra memories, but otherwise perfectly healthy!"

"You're sure?" Amy checked. The doctor looked hurt for a second.

"Well of course I'm sure!"

"But you just said it was 'nasty... Ok, ok!" Amy held her hands up in amused surrender when he mock glared at her, rolling her eyes at him. He stuck his tongue out with a sulky pout, making both Anthony and Fae laugh.

"Don't make faces sweetie, if the wind changed you'll be stuck like that."

"River!" Came the delighted cries, making River smile tiredly. She shifted, looking around her in confusion.

"How on earth did I get here?" She asked hoarsely. Amy passed her a glass of water, which she drank gratefully as they explained what had happened. "But… how did she know about the cracks? Nobody's supposed to remember. And no offence, but why abduct AJ and Fae- we don't even know them."

"We're from your future. I think Kovarian got a little mixed up ." Supplied AJ. River rolled her eyes.

"Wonderful. Ripping apart the universe because she made a mistake." She muttered, settling back against the cushions. The doctor was laying beside her, with Amy sitting cross legged on the end of the bed and Rory perching next to her.

"And we have no idea how she remembered. Theoretically, it's not possible." Rory sighed, linking his hand with Amy's. They fell silent, until a tentative voice sounded at the door.

"Amelia?" Amy looked around to find her mother hovering uncertainly at the doorway.

"Mum! Come on in." she smiled. She noticed River tensing out of the corner of her eye, and smiled comfortingly at her.

"Mum, this is our River." She introduced. River smiled weakly.

"Hi Mrs Pond." She said sheepishly, guessing that Amy had explained who she was by the astonished wonder on Agatha's face. "Sorry about the china set."

At this, Agatha let out an amazed laugh. "Mels. It really is you."

"Sorry about that. Bet you thought you'd got rid of me, huh?" she joked feebly. Agatha looked horrified.

"No! Of course not!" she cried. "It's… somewhat… a surprise. But a welcomed one! After all, I live in Leadworth- we dance with imaginary childhood friends at weddings!"

River and Amy burst into laughter at this, while Rory just shook his head in amusement.

"What?" Clara murmured softly, mystified. The doctor bounced over to her, wrapping an arm around her shoulders.

"It's a bit of a long story." He met Rivers' eyes, and grinned cheekily at her. She smiled back warily as she sat up fully, brow furrowing as she watched. "A very long story and I don't know some of it. One that…well… It can't be told. Has to be lived."

River threw back her head, and laughed.


	6. Chapter 6

"Can't you come home?" Agatha pleaded with Amy. The redhead shook her head sadly.

"I'm sorry. The timelines..." She started. Agatha made a small sound of distress.

"You've been travelling with the doctor too long." AJ said lazily. They were in the console room, and she was perched on the railing, legs swinging.

"What?" Amy asked. AJ sighed.

"Seriously? The only fixed point is that you and Rory die in 19 whatever. Presumably, for this to happen you must live in the same time period, but that doesn't mean you have to spend the rest of your lives trapped there! Jeez." She muttered the last word under her breath, rolling her eyes slightly.

"But... The tardis can't land in New York. Too many paradoxes." Amy said confusedly.

"... Really?" AJ looked at them in disbelief. "A bus. A train. A car. All perfectly good forms of transport that can get you beyond the city limits."

She noticed them staring at her. "What? It's obvious! Honestly."

"We really have been travelling with him too long." Amy sighed. "We're idiots."

"Yep." AJ agreed cheerfully. She bounced up from her seat, making her way outside the tardis where Rory, Brian, River and the doctor were exploring the complex they'd been kept in while Fae and Anthony played with Clara.

"Reminds me a bit of demons run." Commented River, looking around. Rory made a small sound in the back of his throat, making her wince and shoot him an apologetic look. As they were talking, AJ heard a crack coming from the next room over and peered around the corner, smiling slightly when she saw the source of the sound and gestured to Fae, who left Clara to run to catch up with her sister. They slipped silently from the room, Fae squealing happily as she caught sight of the woman standing in the centre of the destruction.

"Mummy!" She ran into the woman's arms and hugged her fiercely. AJ stood back and watched, painfully aware she didn't feel the usual joy at seeing her mum.

"Hello darlings." River Song smiled. She looked over at AJ- who was standing staring at the floor- in confusion, before reluctant realisation dawned and she gently lowered Fae to the floor.

"Sweetheart, could you go fetch Amy and Rory for me? Don't let the others know." Fae nodded eagerly, scampering off to the other room. None noticed the hidden figure in the shadows.

"AJ?" River approached the teenager, who ducked her head lower. "AJ."

When the girl didn't answer, she sighed, and slipped her arms around her. "Sweetheart, please."

AJ shuddered suddenly, letting out a strangled sob as she turned into the embrace, clinging to her mum desperately.

"You didn't know us. You didn't even know us. Why didn't you warn me?!" She choked out, and River hugged her tighter.

"I'm sorry. I was going to, but I didn't realise how soon... I'm sorry." She murmured. AJ shook as she held on tightly, pressing her face into her mothers shoulder.

"Please don't leave me." She whispered, so softly it was almost impossible to hear her.

"Never." River promised gently. They held on tightly to each other, until Amy and Rory came in, Fae tugging at them impatiently.

"Alright, we're coming!" Laughed Amy. The smile faded from her face as she caught sight of River and AJ, who pulled away as they entered, wiping the tears from her cheeks before turning around to face them.

"River! Oh... I, ah..." The pair glanced at each other, casting worried looks behind them as they remembered who was standing in the other room.

"Hello mum, dad. Don't worry, I'm older, already lived through this." River assured them, kissing each of them on the cheek.

"Oh. Wait, I don't understand." Rory said, confused. "Why are you here?"

"You didn't tell them?" River muttered over her shoulder to AJ.

"Tell them how? Technically, I'm only a little over a decade younger them!" She protested, rolling her eyes.

"Tell us what?" Rory interrupted them, sensing the argument was about to escalate. River frowned.

"Mother, father, may I introduce my daughters, Amelia Joy and Fae Idris Song. They- unfortunately- inherited the gene that seems to get all of our dysfunctional family in trouble." River smiled affectionately at them both as she lifted Fae onto her hip. Amy and Rory gaped, mouths opening and closing repeatedly.

"Daughter. As in yours and... The doctors?" Amy said weakly after a while. River nodded, slipping her arm around AJ's shoulders as she did so.

"Hang on, you mean this whole time you knew we were your... Grandparents?" Rory tried to get his head around it. AJ inclined her head slightly.

"Sorry. Not exactly something you bring up in a normal conversation, is it?" She grimaced slightly at the thought of that. Amy suddenly groaned slightly.

"Oh my god. Anthony's younger than both of you! Your uncle is young enough to be your little brother!" Fae giggled at this as Amy sat down heavily on a nearby piece of debris, rubbing her head with her hand while Rory simply stood and scratched his head. River smiled at them as they worked out the timelines in their heads, playing with AJ's hair absently.

"When did you start to straighten it?" She asked suddenly, fingers catching on a stray lock that had fallen from her braid.

"When the wrong people started asking the wrong questions." AJ answered with a sad smile. "Not many people have hair like ours. It was getting too difficult to hide who I was."

"Hide?" Rory questioned.

"It's not difficult to work out that if we're River Songs daughters, then we're also the doctors. And a children of the last time lords in existence were always going to be in danger, so only people we trust know our real identities." AJ's voice was nonchalant, but even the clueless Rory could see the pain hidden behind her casualness.

"Mum, dad, I'm sorry but we have to go. The doctor could walk in any second." River said quietly. Amy looked up sadly.

"Will we ever see you again?" She asked.

"Course! I'm in the other room, aren't I?" River smiled with difficult. Amy shook her head, standing to make her way over to her daughter.

"No, I mean this you. Old enough to know what happened to our father and I, with two daughters and a never-ending ability to induce heart attacks..." Amy trailed off as River simply hugged her.

"I don't know, but it's unlikely. We will always be thinking of you though- these two were raised on your books, mother." Amy laughed at this.

"Well then, I'll write lots more. Look for the afterwords and such, because they'll be for all of you." She promised, hugging Fae and AJ as River embraced Rory.

"Stay out of trouble, won't you?" He implored her, causing her to laugh loudly.

"Oh, daddy, this is me we're talking about!" She kissed his cheek before stepping and holding out her hand to AJ, who swung Fae onto her hip and slipped her arm through Rivers.

"Say bye to the old man and Clara for us, won't you?" The teenager grinned. Before they could answer, River typed in the final coordinate and the three disappeared with a bright flash that caused Amy and Rory to blink in surprise.

"Well... That was different." Rory commented they stared at the now empty spot. Slowly, with knowing smiles, they linked fingers and made their way back into the other room. After they'd left, Clara stepped out of the shadows where she'd been hidden with a stunned thoughtfulness on her face. She'd been worried when Fae had run off without a word, and followed her, hiding when curiosity got the better of her. By the time she realised the moment should be private, it was too late to make her escape. But even when she hadn't been travelling with the doctor for that long, she realised how much danger the two girls were in, especially if anyone found out about their heritage and who their father was. No, she thought. She would keep their secret, and take it to the grave with her.

She entered the tardis stealthily, leaning against the railing as she watched the doctor show Anthony around the console.

"Where are Fae and AJ? It's about time we all got home." The man in question looked up.

"They already did. Got a ride from their mum. They said to tell you bye, though." Amy said quickly. The doctor looked faintly disappointed of a moment, before shaking it off easily.

"Well then, two less to worry about." He said cheerily.

"Make that four less sweetie. I have to get mum, dad and Anthony back to New York, which you can't do in the tardis." River kissed him on the cheek gently, stepping back while her parents said their goodbyes and taking first Amy and her brother, then her father back to their home on Manhattan. The doctor, for his part, flew the elder Ponds and Williams back home, dropping the off minutes after they'd first been taken. Finally, it was just him and Clara on the ship.

"That was... Interesting." Clara said, flopping onto a seat. The doctor looked at her.

"I was going to say exhausting, but yes, interesting covers it." He said. They looked at each other for a long moment, before bursting into laughter.

"So much for the quiet day out." Managed Clara. The doctor bounced up to the console.

"Quiet day out. I can do that! Or maybe… home?" Clara nodded at him from her seat, and he executed a perfect bow. He spun a wheel and flipped a lever as the tardis rumbled and they both grabbed on tight. Clara laughed as they were thrown around, and the doctor smiled.

"Geronimo!"

_**There we go! The sequel- called 'The Luna Disease'- will be out later today or tomorrow. Tell me if you liked this one?**_

_**Here's a sneak peak of the next story:**_

_"So... Where are we going?" Clara grinned as the doctor slid around the console, pulling levers and spinning wheels._

_"The third moon of Laxtri! You'll love it- the sky is actually green! And the people!" They landed with a large bump, and he gestured towards the doors. "After you, Miss Oswald."_

_Clara grinned as she bounced towards the doors and flung them open, before pausing._

_"Er... Doctor? The sky is... Not green." The doctor peered over her shoulder as she looked at him skeptically._

_"Ah... Sorry." He winced. Clara sighed._

_"Where are we?"_

_"The moon! In the 51st century! How did we...?" He spun to look at the console, but Clara stepped out, smiling as she stared around her. _

_"Wow..." She murmured. "Wait, how are we breathing? And how is there sunlight?"_

_"Artificial sunlight and atmosphere! You lot are clever aren't you. There's a whole colony of humans here- hospitals, schools, offices, homes, even a university! An entire world, on the moon." He grinned at her, but the smile faded as he caught sight of the armed guards marching towards them._

_"Oh, that's extremely not good." He muttered as they surrounded them._

_"You will come with us. Do not resist, or force will be used." A mechanical voice said._

_"Robots!? Robot soldiers! On the moon!" The doctor laughed as he held his hands up in the air._

**_X_**


End file.
